Edaphic fauna and physico-chemical atributes of soil in different phytophysionomies of Cerrado

ABSTRACT The edaphic community comprises several organisms that perform ecological functions in the environment, such as litter fragmentation, nutrient cycling, and modifications of soil structure, in addition to acting as food chain regulators. Thus, the objective of this study was to evaluate the composition of the edaphic fauna and the physical and chemical attributes of soil in different physiognomies of Cerrado in the Parque Estadual do Mirador (PEM). The study was carried out in two Cerrado formations (Sparse Cerrado and Typical Cerrado) in PEM, where 100 pitfall traps were installed. The edaphic organisms were screened and identified in terms of orders, suborders, subfamilies, families, abundance, richness, Shannon diversity, and Pielou’s equitability. A total of 4,149 individuals were collected from two experimental plots. The plot in the Typical Cerrado showed greater taxonomic richness (25 groups) and greater Shannon diversity (H’ = 1.65), while the plot in Sparse Cerrado presented 19 edaphic groups and Shannon diversity equal to H’ = 1.51. The factorial exploration explained 84.43% of the original data from the Sparse Cerrado and 90.84% from the Typical Cerrado. It is concluded that the plot in the Typical Cerrado showed greater differences in terms of richness and abundance due to the more favorable conditions for soil fauna, such as a high content of organic material and greater vegetation cover.

Age and injury size influence the magnitude of fecal dysbiosis in adult burn patients

Clinical studies have demonstrated that age ≥ 50 years old is an independent risk factor associated with poor prognosis after burn injury, the second leading cause of traumatic injuries in the aged population. While mechanisms driving age-dependent post-burn mortality are perplexing, changes in the intestinal microbiome however may contribute to the heightened, dysregulated systemic response seen in aging burn patients. The fecal microbiome from 22 patients admitted to a verified burn center from July 2018 to February 2019 were stratified based on age of 50 years and total burn surface area (TBSA) size of ≥10%. Significant differences (P = 0.014) in overall microbiota community composition (i.e., beta diversity) were measured across the four patient groups, young <10% TBSA, young ≥10% TBSA, older <10% TBSA, and older ≥10% TBSA. Differences in beta diversity were driven by %TBSA (P = 0.013) and trended with age (P = 0.087). Alpha diversity components, richness, evenness, and Shannon diversity were measured. We observed significant differences in bacterial species evenness (P = 0.0023) and Shannon diversity (P = 0.0033) between the groups. There were significant correlations between individual bacterial species and levels of SCFA. Specifically, levels of fecal butyrate correlated with the presence of Enterobacteriaceae, an opportunistic gut pathogen, when elevated in burn patients lead to worsen outcomes. Overall, our findings reveal that age-specific changes in the fecal microbiome following burn injuries may contribute to immune system dysregulation in patients with varying TBSA burns and potentially lead to worsen clinical outcomes with heightened morbidity and mortality.

Floristic Composition, Diversity and Plant Community Along Elevational Gradients in the Afro-alpine Vegetation of Abohoy Gara Mountain, northern Ethiopia

This research was conducted in Afro-alpine vegetation of Abohoy Gara Mountain in northern Ethiopia with the aim of analyzing floristic composition along elevational gradients, threats and conservation methods. Data were collected from 53 quadrats (15 m x 15 m) laid at 100 m interval along parallel vertical transects spaced at 500m to each other to record shrubs and trees, whereas 1 m x 1 m plots were used to record herbs. Cover abundance data were used to do community analysis using R version 3.1.2 software. Analysis of variance (ANOVA) was employed to determine significant level of species richness; abundance and Shannon diversity index along elevational gradient, whereas pearson’s correlation test was applied to check the relationship between environmental variables with species richness, species abundance and Shannon diversity index (H’) using SPSS v20. Ninety-seven plant species composed of 82 genera under 40 families were recorded. The mean number of plant species showed significant difference along elevational gradient (P < 0.05). Besides, significant (P < 0.05) negative correlation of elevation with the plant richness, abundance as well as Shannon diversity index had been observed. Based on dominant species, a total of five plant communities were identified. The maximum plant diversity occurred in community type III (3.79), whereas the least plant diversity occurred in community type IV and community type V. Vegetation cover and species composition of Abohoy Gara Mountain is being endangered by agricultural expansion, over grazing and logging of wood for construction material. Hence, it needs application of complementary on-site and offsite conservation approaches. This calls for further joint management of the Abohoy Gara Mountain by the local people and administrative bodies in the overall conservation actions that can save and rehabilitate the plant resources and their habitats.

Spatial variability and environmental drivers of cassava—arbuscular mycorrhiza fungi (AMF) associations across Southern Nigeria

Cassava, forming starch-rich, tuberous roots, is an important staple crop in smallholder farming systems in sub-Saharan Africa. Its relatively good tolerance to drought and nutrient-poor soils may be partly attributed to the crop’s association with arbuscular mycorrhiza fungi (AMF). Yet insights into AMF-community composition and richness of cassava, and knowledge of its environmental drivers are still limited. Here, we sampled 60 cassava fields across three major cassava-growing agro-ecological zones in Nigeria and used a DNA meta-barcoding approach to quantify large-scale spatial variation and evaluate the effects of soil characteristics and common agricultural practices on AMF community composition, richness and Shannon diversity. We identified 515 AMF operational taxonomic units (OTUs), dominated by Glomus, with large variation across agro-ecological zones, and with soil pH explaining most of the variation in AMF community composition. High levels of soil available phosphorus reduced OTU richness without affecting Shannon diversity. Long fallow periods (> 5 years) reduced AMF richness compared with short fallows, whereas both zero tillage and tractor tillage reduced AMF diversity compared with hoe tillage. This study reveals that the symbiotic relationship between cassava and AMF is strongly influenced by soil characteristics and agricultural management and that it is possible to adjust cassava cultivation practices to modify AMF diversity and community structure. Graphical abstract

Habitation Sites Influence Tree Community Assemblages in the Great Bear Rainforest, British Columbia, Canada

Identifying how past human actions have influenced their environment is essential for understanding the ecological factors that structure contemporary ecosystems. Intertidal resource use by Indigenous Peoples for thousands of years has led to habitation sites containing vast shell midden deposits and facilitating long-term impacts on soil chemistry and drainage. Here we examine how these shell middens have impacted various forest metrics, such as species diversity, community composition, canopy height, and regeneration recruitment to determine if forests on habitation sites differ from the surrounding matrix. We surveyed known habitation sites with archeological evidence indicating past year-round human occupation, within the Hakai Lúxvbálís Conservancy on Calvert and Hecate Islands within the Great Bear Rainforest along British Columbia’s Central Coast. Our results demonstrate that habitation sites exhibit lower tree species richness, less relative species abundances, as such, displayed lower Shannon diversity and inverse Simpson values. The composition of tree communities on habitation sites was statistically different, with western hemlock and western redcedar densities increasing on non-habitation sites. Conversely, regeneration diversity at habitation sites was more even and exhibited elevated Shannon diversity and inverse Simpson values. The community composition of regeneration was more consistent among habitation and non-habitation sites; however, western redcedar, western hemlock and Sitka spruce were more abundant at habitation sites. For all tree species, maximum height was higher within the habitation sites; however, this trend was the most notable in western redcedar and Sitka spruce, which increased by an average of 4.8 m relative to non-habitation sites. Collectively, our findings suggest that long-term habitation alters forest community compositions. The landscape alterations within habitation sites promote conditions needed to support diverse, even, and abundant regeneration communities and consequently increase the height of the dominant coastal tree species. Thus, our results offer evidence that long-term influence by Indigenous communities have a persistent influence on coastal forests.

Gut-Microbiome Composition in Response to Phenylketonuria Depends on Dietary Phenylalanine in BTBR Pahenu2 Mice

Phenylketonuria (PKU) is a metabolic disorder caused by a hepatic enzyme deficiency causing high blood and brain levels of the amino acid Phenylalanine (Phe), leading to severe cognitive and psychological deficits that can be prevented, but not completely, by dietary treatment. The behavioral outcome of PKU could be affected by the gut-microbiome-brain axis, as diet is one of the major drivers of the gut microbiome composition. Gut-microbiome alterations have been reported in treated patients with PKU, although the question remains whether this is due to PKU, the dietary treatment, or their interaction. We, therefore, examined the effects of dietary Phe restriction on gut-microbiome composition and relationships with behavioral outcome in mice. Male and female BTBR Pahenu2 mice received either a control diet (normal protein, “high” Phe), liberalized Phe-restricted (33% natural protein restriction), or severe Phe-restricted (75% natural protein restriction) diet with protein substitutes for 10 weeks (n = 14 per group). Their behavioral performance was examined in an open field test, novel and spatial object location tests, and a balance beam. Fecal samples were collected and sequenced for the bacterial 16S ribosomal RNA (rRNA) region. Results indicated that PKU on a high Phe diet reduced Shannon diversity significantly and altered the microbiome composition compared with wild-type animals. Phe-restriction prevented this loss in Shannon diversity but changed community composition even more than the high-Phe diet, depending on the severity of the restriction. Moreover, on a taxonomic level, we observed the highest number of differentially abundant genera in animals that received 75% Phe-restriction. Based on correlation analyses with differentially abundant taxa, the families Entereococacceae, Erysipelotrichaceae, Porphyromonadaceae, and the genus Alloprevotella showed interesting relationships with either plasma Phe levels and/or object memory. According to our results, these bacterial taxa could be good candidates to start examining the microbial metabolic potential and probiotic properties in the context of PKU. We conclude that PKU leads to an altered gut microbiome composition in mice, which is least severe on a liberalized Phe-restricted diet. This may suggest that the current Phe-restricted diet for PKU patients could be optimized by taking dietary effects on the microbiome into account.

Vitamin D Supplementation in Exclusively Breastfed Infants Is Associated with Alterations in the Fecal Microbiome

Breastfeeding and introduction of solid food are the two major components of infant feeding practices that influence gut microbiota composition in early infancy. However, it is unclear whether additional factors influence the microbiota of infants either exclusively breastfed or not breastfed. We obtained 194 fecal samples from infants at 3–9 months of age, extracted DNA, and sequenced the V4 region of the 16S rRNA gene. Feeding practices and clinical information were collected by questionnaire and abstraction of birth certificates. The gut microbiota of infants who were exclusively breastfed displayed significantly lower Shannon diversity (p-adjust < 0.001) and different gut microbiota composition compared to infants who were not breastfed (p-value = 0.001). Among the exclusively breastfed infants, recipients of vitamin D supplements displayed significantly lower Shannon diversity (p-adjust = 0.007), and different gut microbiota composition structure than non-supplemented, breastfed infants (p-value = 0.02). MaAslin analysis identified microbial taxa that associated with breastfeeding and vitamin D supplementation. Breastfeeding and infant vitamin D supplement intake play an important role in shaping infant gut microbiota.

Randomized controlled trial of gut decontamination in pediatric patients undergoing allogeneic hematopoietic stem cell transplantation

Background. Gut decontamination (GD) can decrease the incidence and severity of acute graft-versus-host-disease (aGVHD) in murine models of allogeneic hematopoietic cell transplantation (HCT). Several HCT centers standardly practice GD with different antibiotic regimens. In this pilot study, we examined the impact of GD on the gut microbiome composition and incidence of aGVHD in HCT patients. Methods. We randomized 20 pediatric patients undergoing allogeneic HCT to receive (GD) or not receive (no-GD) oral vancomycin-polymyxin B from day -5 through neutrophil engraftment. We evaluated shotgun metagenomic sequencing of serial stool samples to compare the composition and diversity of the gut microbiome between study arms. We assessed clinical outcomes in the 2 arms and performed strain-specific analyses of pathogens that caused bloodstream infections (BSI). Results. The two arms did not differ in Shannon diversity of the gut microbiota at two weeks post-HCT (Genus, p=0.8; Species, p=0.44) or aGVHD incidence (p=0.58). Immune reconstitution of T-cell subsets was similar, but absolute CD19+ B-cell counts were higher in the GD arm at 12 months post-HCT (p=0.02). Five patients in the no-GD arm had eight BSI episodes vs one episode in the GD arm (p=0.09). The BSI-causing pathogens were traceable to the gut in seven of eight BSI episodes in the no-GD arm, including the genus Staphylococcus. Conclusions. While GD did not differentially impact Shannon diversity or clinical outcomes, our findings suggest that GD may protect against gut-derived BSI in HCT patients by decreasing the prevalence or abundance of gut microbial pathogens. Trial Registration. ClinicalTrials.gov NCT02641236 Funding. Damon Runyon Cancer Research Foundation, V Foundation, Sloan Foundation, Emerson Collective, Stanford MCHRI, NIH-R01-AI143757, R01-AI148623, S100D023452, 1S10OD02014101, T32-DK098132.

Association Between Neonatal Gut Microbiome and Infant Wheeze

Background: Asthma is a chronic respiratory disease that affects 10% of children. Infant wheeze at 1 year and the subsequent development of asthma in early childhood has been associated with infant gut dysbiosis. However, little is known about the relationship between neonatal gut microbiome and the development of wheeze during the first 18 months of life. We hypothesize that the gut microbiome at birth and throughout the first 18 months of life is associated with infant wheeze. Project Methods: Stool samples were collected from infants at birth, 1, 3, and 12 months of age. The Illumina Miseq system was used to sequence the bacterial V4 region of 16S-rRNA gene. Mothur software was used for analysis. Statistical analysis was used to measure stool shannon diversity and evenness as they relate to timepoint and wheeze vs no wheeze groups. Results: The study population consisted of 28 infants (18 males and 10 females). 11% of participants reported they had been diagnosed with wheeze by a physician (n=3). Statistical analysis of shannon diversity showed no differences in the stool between participants who wheeze vs those who do not wheeze (p=0.78). No difference in stool evenness was detected between participants who reported wheeze vs no wheeze (p=0.71). However, this analysis includes multiple timepoints. Analysis of stool shannon diversity across timepoints did show a significant difference in stool microbiome (p=0.01). Conclusion: No differences in stool microbiome were found between infants who do not wheeze and those who do. Further studies can investigate a greater number of samples at each timepoint and relate these to objective measures such as pulmonary function tests. Understanding the association between infant gut dysbiosis and wheeze could have implications for predicting development of asthma in early childhood and potentially lead to targeted interventions.

Investigation of the impact of commonly used medications on the oral microbiome of individuals living without major chronic conditions

Background Commonly used medications produce changes in the gut microbiota, however, the impact of these medications on the composition of the oral microbiota is understudied. Methods Saliva samples were obtained from 846 females and 368 males aged 35–69 years from a Canadian population cohort, the Atlantic Partnership for Tomorrow’s Health (PATH). Samples were analyzed by 16S rRNA gene sequencing and differences in microbial community compositions between nonusers, single-, and multi-drug users as well as the 3 most commonly used medications (thyroid hormones, statins, and proton pump inhibitors (PPI)) were examined. Results Twenty-six percent of participants were taking 1 medication and 21% were reported taking 2 or more medications. Alpha diversity indices of Shannon diversity, Evenness, Richness, and Faith’s phylogenetic diversity were similar among groups, likewise beta diversity as measured by Bray-Curtis dissimilarity (R2 = 0.0029, P = 0.053) and weighted UniFrac distances (R2 = 0.0028, P = 0.161) were non-significant although close to our alpha value threshold (P = 0.05). After controlling for covariates (sex, age, BMI), six genera (Saprospiraceae uncultured, Bacillus, Johnsonella, Actinobacillus, Stenotrophomonas, and Mycoplasma) were significantly different from non-medication users. Thyroid hormones, HMG-CoA reductase inhibitors (statins) and PPI were the most reported medications. Shannon diversity differed significantly among those taking no medication and those taking only thyroid hormones, however, there were no significant difference in other measures of alpha- or beta diversity with single thyroid hormone, statin, or PPI use. Compared to participants taking no medications, the relative abundance of eight genera differed significantly in participants taking thyroid hormones, six genera differed in participants taking statins, and no significant differences were observed with participants taking PPI. Conclusion The results from this study show negligible effect of commonly used medications on microbial diversity and small differences in the relative abundance of specific taxa, suggesting a minimal influence of commonly used medication on the salivary microbiome of individuals living without major chronic conditions.